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DOE OSTI2020

Development of neural network force fields for corrosion studies

To fully understand the chemistry and physics of corrosion, novel methods of simulation must be developed. One approach is designing machine learning (ML) algorithms integrated with density functional theory to develop adaptive force fields to gain insight into corrosion behavior namely at the surface of metal oxides. Current methods of modeling corrosion are slow due to the computational cost of resolving both reaction mechanics and mass transport processes. Machine learning methods can be implemented to obtain structure-activity relationships at both the molecular and bulk scale while still retaining the accuracy of density functional theory (DFT) and significantly decreasing the time needed for simulations of complex chemical processes in the various environments of corrosion. Multiscale models are needed for corrosion studies to fully understand its processes not only at the atomic length scale (chemical bonding, energies, and forces), but also at the nano and meso length scales (solid-state physics and material science processes). Current methods of study include DFT, molecular dynamics, and Monte Carlo. The limitation of DFT is that only a small number of atoms or molecules can be simulated at that level of theory. Density functional theory is used to study the electronic structure of atoms and molecules, and calculate the force component of each atom. However, these calculations are limited to about 1000 atoms. Custom periodic boundary conditions (PBC) can be used to describe the various environments and defects that affect the atomic forces to produce a large data set from which a training set can be derived. Machine learning can be utilized to overcome the barrier of modeling macroscopic and multi-scale processes from ab initio calculations through the development of adaptive force fields. Local environments determine the atomic forces of a given system, therefore adaptive force fields must be created to produce reliable quantum mechanical calculations. This can be achieved by developing a learning algorithm that uses the mapped atomic forces or fingerprint as an input to produce energies and magnetic moments as output. A systematic approach was used to begin to build a data set in order to accurately describe the atomic forces in various environments. In Figure 4 below, a simple PBC cell of Fe{sub 2}O{sub 3} was first optimized. A surface optimization was performed next, followed by a hydroxylated surface optimization. Once this calculation has converged, the adsorption of halide species to the hydroxylated surface will be investigated. TensorFlow is an open source platform for machine learning developed by Google. Using a high level application program interface (API) such as Keras allows for building and training ML models easily in a number of different environments and languages. For this project, a neural network was developed within Anaconda in Python. Future Work: Further development of reference data set; Refining neural network and learning algorithm; Fingerprinting atomic environment to enable mapping of atomic force components; Choosing appropriate training set from reference data; Learning from training set and enabling non-linear mapping of training set fingerprints and the atomic forces; Estimation of uncertainty to identify ranges of outside applicability; Testing and analysis of molecular dynamic simulations.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Constraining chaos: Enforcing dynamical invariants in the training of reservoir computers

Drawing on ergodic theory, we introduce a novel training method for machine learning based forecasting methods for chaotic dynamical systems. The training enforces dynamical invariants—such as the Lyapunov exponent spectrum and the fractal dimension—in the systems of interest, enabling longer and more stable forecasts when operating with limited data. The technique is demonstrated in detail using reservoir computing, a specific kind of recurrent neural network. Finally, results are given for the Lorenz 1996 chaotic dynamical system and a spectral quasi-geostrophic model of the atmosphere, both typical test cases for numerical weather prediction.

97 MATHEMATICS AND COMPUTING↗

NASA NTRSDate not supplied

Adaptive Learning for Reliability Analysis using Support Vector Machines

A novel algorithm is presented for adaptive learning of an unknown function that separates two regions of a domain.In the context of reliability analysis these two regions represent the failure domain, where a set of constraints or requirements are violated, and a safe domain where they are satisfied. The Limit State Function (LSF) separates these two regions. Evaluating the constraints for a given parameter point requires the evaluation of a computational model that may well be expensive. For this reason we wish to construct a meta-model that can estimate the LSFas accurately as possible, using only a limited amount of training data. This work presents an adaptive strategy employing a Support Vector Machine (SVM) as a meta-model to provide a semi-algebraic approximation of the LSF.We describe an optimization process that is used to select informative parameter points to add to training data at each iteration to improve the accuracy of this approximation. A formulation is introduced for bounding the predictions of the meta-model; in this way we seek to incorporate this aspect of Gaussian Process Models (GPMs) within anSVM meta-model. Finally, we apply our algorithm to two benchmark test cases, demonstrating performance that is comparable with, if not superior, to a standard technique for reliability analysis that employs GPMs

Adaptive learning↗

DOE OSTI2025

Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida

Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obtain the titers, rates and yields needed for commercial viability. Here, we present a molecule- and host-agnostic active learning process for media optimization that is enabled by a fast and highly repeatable semi-automated pipeline. Its application yielded 60% and 70% increases in titer, and 350% increase in process yield in three different campaigns for flaviolin production in Pseudomonas putida KT2440. Explainable Artificial Intelligence techniques pinpointed that, surprisingly, common salt (NaCl) is the most important component influencing production. The optimal salt concentration is very high, comparable to seawater and close to the limits that P. putida can tolerate. The availability of fast Design-Build-Test-Learn (DBTL) cycles allowed us to show that performance improvements for active learning are rarely monotonous. This work illustrates how machine learning and automation can change the paradigm of current synthetic biology research to make it more effective and informative, and suggests a cost-effective and underexploited strategy to facilitate the high titers, rates and yields essential for commercial viability.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Ion correlations explain kinetic selectivity in diffusion-limited solid-state synthesis reactions

Establishing viable solid-state synthesis pathways for novel inorganic materials remains a major challenge in materials science. Previous pathway design methods using pairwise reaction approaches have navigated the thermodynamic landscape with first-principles data but lack kinetic information, limiting their effectiveness. This gap leads to suboptimal precursor selection and predictions, especially for reactions forming competing phases with similar formation energies, where ion diffusion is a critical influence. Here we demonstrate an inorganic synthesis framework by incorporating machine learning-derived transport properties through ‘liquid-like’ product layers into a thermodynamic cellular reaction model. In the Ba–Ti–O system, known for its competitive polymorphism, we obtain accurate predictions of phase formation with varying BaO:TiO2 ratios as a function of time and temperature. We find that diffusion–thermodynamics interplay governs phase compositions, with cross-ion transport coefficients critical for predicting diffusion-limited selectivity. This work bridges length scales and timescales by integrating solid-state reaction kinetics with first-principles thermodynamics and spatial reactivity.

Atomistic models↗

DOE OSTI2020

QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants

Linkage mapping has been widely used to identify quantitative trait loci (QTL) in many plants and usually requires a time-consuming and labor-intensive fine mapping process to find the causal gene underlying the QTL. Previously, we described QTG-Finder, a machine-learning algorithm to rationally prioritize candidate causal genes in QTLs. Although it showed good performance, QTG-Finder could only be used in Arabidopsis and rice because of the limited number of known causal genes in other species. Here we tested the feasibility of enabling QTG-Finder to work on species that have few or no known causal genes by using orthologs of known causal genes as training set. The model trained with orthologs could recall about 64% of Arabidopsis and 83% of rice causal genes when the top 20% ranked genes were considered, which is similar to the performance of models trained with known causal genes. The average precision was 0.027 for Arabidopsis and 0.029 for rice. We further extended the algorithm to include polymorphisms in conserved non-coding sequences and gene presence/absence variation as additional features. Using this algorithm, QTG-Finder2, we trained and cross-validated Sorghum bicolor and Setaria viridis models. The S. bicolor model was validated by causal genes curated from the literature and could recall 70% of causal genes when the top 20% ranked genes were considered. Furthermore, we applied the S. viridis model and public transcriptome data to prioritize a plant height QTL and identified 13 candidate genes. QTL-Finder2 can accelerate the discovery of causal genes in any plant species and facilitate agricultural trait improvement.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Machine learning the electric field response of condensed phase systems using perturbed neural network potentials

Abstract The interaction of condensed phase systems with external electric fields is of major importance in a myriad of processes in nature and technology, ranging from the field-directed motion of cells (galvanotaxis), to geochemistry and the formation of ice phases on planets, to field-directed chemical catalysis and energy storage and conversion systems including supercapacitors, batteries and solar cells. Molecular simulation in the presence of electric fields would give important atomistic insight into these processes but applications of the most accurate methods such as ab-initio molecular dynamics (AIMD) are limited in scope by their computational expense. Here we introduce Perturbed Neural Network Potential Molecular Dynamics (PNNP MD) to push back the accessible time and length scales of such simulations. We demonstrate that important dielectric properties of liquid water including the field-induced relaxation dynamics, the dielectric constant and the field-dependent IR spectrum can be machine learned up to surprisingly high field strengths of about 0.2 V Å −1 without loss in accuracy when compared to ab-initio molecular dynamics. This is remarkable because, in contrast to most previous approaches, the two neural networks on which PNNP MD is based are exclusively trained on molecular configurations sampled from zero-field MD simulations, demonstrating that the networks not only interpolate but also reliably extrapolate the field response. PNNP MD is based on rigorous theory yet it is simple, general, modular, and systematically improvable allowing us to obtain atomistic insight into the interaction of a wide range of condensed phase systems with external electric fields.

Science & Technology - Other Topics↗

DOE OSTI2026

Modeling Single-Crystal Battery Materials: From Fundamental Understanding to Performance Evaluation

The performance of rechargeable batteries is fundamentally influenced by the physicochemical properties and microstructural features of their key material components. Recent experimental advancements have highlighted the potential of single-crystal (SC) morphologies to address inherent limitations of polycrystalline (PC) electrodes and solid-state electrolytes, offering tunable charge transport kinetics and improved cell cycling performance. Here, this review examines how state-of-the-art computational modeling, from atomistic and mesoscale to continuum-level approaches, including machine learning methodologies, has been utilized to investigate the critical factors governing the electrochemical behavior of SC battery materials. We explore how predictive modeling can elucidate the processing–structure–property–performance relationships of SC cathodes, anodes, and solid-state electrolytes, with a focus on unique SC characteristics such as crystallographic anisotropy, size effects, and facet-dependent properties. Additionally, we identify limitations in commonly used modeling techniques and discuss strategies to address these challenges. By integrating high-fidelity simulations with experimental insights, this review aims to outline a clear path for the rational design and optimization of SC battery components, paving the way for accelerated advancements in energy storage technologies.

Materials science↗

DOE OSTI2023

Field evaluation of semi‐automated moisture estimation from geophysics using machine learning

Geophysical methods can provide three-dimensional (3D), spatially continuous estimates of soil moisture. However, point-to-point comparisons of geophysical properties to measure soil moisture data are frequently unsatisfactory, resulting in geophysics being used for qualitative purposes only. This is because (1) geophysics requires models that relate geophysical signals to soil moisture, (2) geophysical methods have potential uncertainties resulting from smoothing and artifacts introduced from processing and inversion, and (3) results from multiple geophysical methods are not easily combined within a single soil moisture estimation framework. To investigate these potential limitations, an irrigation experiment was performed wherein soil moisture was monitored through time, and several surface geophysical datasets indirectly sensitive to soil moisture were collected before and after irrigation: ground penetrating radar, electrical resistivity tomography (ERT), and frequency domain electromagnetics (FDEM). Data were exported in both raw and processed form, and then snapped to a common 3D grid to facilitate moisture prediction by standard calibration techniques, multivariate regression, and machine learning. A combination of inverted ERT data, raw FDEM, and inverted FDEM data was most informative for predicting soil moisture using a random regression forest model (one-thousand 60/40 training/test cross-validation folds produced root mean squared errors ranging from 0.025–0.046 cm 3 /cm 3 ). This cross-validated model was further supported by a separate evaluation using a test set from a physically separate portion of the study area. Machine learning was conducive to a semi-automated model-selection process that could be used for other sites and datasets to locally improve accuracy.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Intensity of sample processing methods impacts wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes

Wastewater SARS-CoV-2 surveillance has been deployed since the beginning of the COVID-19 pandemic to monitor the dynamics in virus burden in local communities. Genomic surveillance of SARS-CoV-2 in wastewater, particularly efforts aimed at whole genome sequencing for variant tracking and identification, are still challenging due to low target concentration, complex microbial and chemical background, and lack of robust nucleic acid recovery experimental procedures. The intrinsic sample limitations are inherent to wastewater and are thus unavoidable. Here, we use a statistical approach that couples correlation analyses to a random forest-based machine learning algorithm to evaluate potentially important factors associated with wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes, with a specific focus on the breadth of genome coverage. We collected 182 composite and grab wastewater samples from the Chicago area between November 2020 to October 2021. Samples were processed using a mixture of processing methods reflecting different homogenization intensities (HA + Zymo beads, HA + glass beads, and Nanotrap), and were sequenced using one of the two library preparation kits (the Illumina COVIDseq kit and the QIAseq DIRECT kit). Technical factors evaluated using statistical and machine learning approaches include sample types, certain sample intrinsic features, and processing and sequencing methods. The results suggested that sample processing methods could be a predominant factor affecting sequencing outcomes, and library preparation kits was considered a minor factor. Finally, a synthetic SARS-CoV-2 RNA spike-in experiment was performed to validate the impact from processing methods and suggested that the intensity of the processing methods could lead to different RNA fragmentation

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Leveraging unlabeled SEM datasets with self-supervised learning for enhanced particle segmentation

Scanning Electron Microscopes (SEMs) are widely used in experimental science laboratories, often requiring cumbersome and repetitive user analysis. Automating SEM image analysis processes is highly desirable to address this challenge. In particle sample analysis, Machine Learning (ML) has emerged as the most effective approach for particle segmentation. However, the time-intensive process of manually annotating thousands of SEM images limits the applicability of supervised learning approaches. Self-Supervised Learning (SSL) offers a promising alternative by enabling knowledge extraction from raw, unlabeled data. This study presents a framework for evaluating SSL techniques in SEM image analysis, focusing on novel methods leveraging the ConvNeXtV2 architecture for particle detection. A dataset comprising 25,000 SEM images is curated to benchmark these proposed SSL methods. The results demonstrate that ConvNeXtV2 models, with varying parameter counts, consistently outperform other techniques in particle detection across different length scales, achieving up to a 34% reduction in relative error compared to established SSL methods. Furthermore, an ablation study explores the relationship between dataset size and SSL performance, providing actionable insights for practitioners regarding model selection and resource efficiency. This research advances the integration of SSL into autonomous analysis pipelines and supports its application in accelerating materials science discovery.

Rettenberger, Luca↗

DOE OSTI2026

Advancing density functional tight-binding method for large organic molecules through equivariant neural networks

Semi-empirical quantum-mechanical (QM) methods have become valuable tools for studying complex (bio)molecular systems due to their balance between computational efficiency and accuracy. A key aspect of these methods is their parameterization, which not only governs the reliability of the results but also provides an opportunity to enhance their overall performance. In our previous work [J. Phys. Chem. Lett., 2021, 11, 16], we advanced the third-order semi-empirical density functional tight-binding (DFTB3) method for computing multiple properties of small molecules by developing the machine learning (ML) potential NN rep to bridge the gap between DFTB3 electronic components and those of the hybrid DFT-PBE0 functional. To overcome the limitations of NN rep , we introduce the EquiDTB framework, which leverages physics-inspired equivariant neural networks (NN) to parameterize scalable and transferable many-body Δ TB potentials, replacing the standard pairwise DFTB repulsive potential. This advancement extends the applicability of our ML-corrected DFTB approach to larger molecules and non-covalent systems (including only C, N, O, and H atoms), going beyond the chemical space represented in the training QM datasets. The enhanced performance of EquiDTB over the standard TB methods is demonstrated by the accurate computation of the atomic forces of S66x8 molecular dimers, as well as their interaction energies. Moreover, EquiDTB can be effectively employed to explore the potential energy surfaces of large and flexible drug-like molecules—for example, to determine the minimum energy path between isomers, analyze structural transitions during dynamical simulations, compute vibrational modes, and investigate energetic rankings. The performance for single molecules slightly decreases when the DFTB electronic energy is reduced to first-order but remains superior to standard TB methods. Our work thus demonstrates that an optimal integration of an equivariant NN with QM datasets can advance the DFTB method while maintaining high efficiency, paving the way for reliable (bio)molecular simulations.

Medrano Sandonas, Leonardo [Technische Universität↗

DOE OSTI2024

Building an ab initio solvated DNA model using Euclidean neural networks

Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

A New Approach for Short-Term Solar Radiation Forecasting Using the Estimation of Cloud Fraction and Cloud Albedo

Solar generation is an increasing part of the energy portfolio in the United States. An accurate forecast of the available solar resource and power is essential to managing the electric grid, market operations, and reducing the cost of solar energy. High-frequency forecasts of solar radiation in intra-hour horizons is important for real-time electric power system energy management, especially at the distribution level. Conventional Numerical Weather Prediction models perform poorly in intra-hour, high-frequency forecasts because of the limits on real-time computing, spatial resolution, and infrequent availability of observations. Although a number of alternative technologies, e.g., time-series analysis and machine learning, have been used to fill this gap, the smart persistence model is among the top-performing models in short-term forecasting and therefore often serves as the baseline to evaluate other forecasting models. Although the smart persistence model often serves as the baseline model in these intra-hour forecasts, obvious uncertainties exist in the current smart persistence model: (1) clear-sky index does not respond to the variation of the solar incident angle when cloud conditions are persistent within the forecast horizon, and (2) cloud coverage is inherently persistent though it is constrained by cloud advection. In this study, we developed a Physics-Based Smart Persistence Model for Intra-Hour Solar Forecasting (PSPI) that integrates cloudy property estimation, a radiative transfer model, and cloud fraction forecasts to improve the performance of the smart persistence model. Compared to the smart persistence model, PSPI does not require additional observations of various atmospheric parameters past global horizontal irradiance, but it is customizable because additional observations, if available, can be ingested to further improve the forecast. Our results show that the PSPI outperforms the persistence and smart persistence model on 5-minute, 15-minute, and 30-minute forecast horizons. The software package of PSPI is flexible to users' needs and provides low computational time to run at site-specific locations across the continental United States.

14 SOLAR ENERGY↗

DOE OSTI2024

Solid-State Mixed-Potential Electrochemical Sensors for Natural Gas Leak Detection and Quality Control (Final Technical Report)

Mitigation of methane emissions are a critical factor to limiting the impact of the natural gas industry on global climate change. Throughout the period of 2020-2024, the University of New Mexico and its commercialization partner and subcontractor, SensorComm Technologies, Inc. (SCT), have worked together to develop a low-cost Artificial Intelligence (AI)-driven Internet of Things (IoT)-based multi-gas sensor platform for methane emissions detection. In the final year of the project, we extended this work to include hydrogen detection in support of a transition to a hydrogen economy where hydrogen could be transported through existing natural gas infrastructure. Mixed potential electrochemical sensors were first prototyped by ceramic additive manufacturing and then transitioned to conventional ceramic manufacturing tape casting and screen-printing technologies in preparation for mass production. Demonstrated limits of detection of 5 ppm of methane in natural gas and 1 ppm of hydrogen were measured. These limits of detection are among the lowest of solid-state electrochemical sensors that have been reported in the literature or available in the industry. Machine learning algorithms were developed to identify natural gas mixtures with > 98% accuracy level and quantify methane concentrations at 97% accuracy. The presence of hydrogen could also be identified, and its concentration quantified at these accuracy levels. These algorithms were optimized for running on portable computing hardware which enabled > 1 Hz processing rates. A portable packaged IoT system was integrated with the electrochemical sensor in collaboration with SCT. The package consists of readout electronics with < 1 mV resolution, sensor temperature control, and data transmission over cellular wireless and/or Wi-Fi networks. Field testing was performed in two rounds at Colorado State University’s Methane Emissions Technology Evaluation Center (CSU METEC). The first round of testing demonstrated successful measurements of methane from an underground natural gas leak of 20 standard liters per minute (SLPM), which agreed with previously published literature using more sophisticated and expensive analytical equipment. The second round of testing showed that an above ground leak of 2 SLPM of hydrogen could be detected at 32 ft. This project has resulted in six published peer reviewed journal articles, over ten presentations at professional conferences, and one full patent application filed in 2023. Future work on this project includes increased sensitivity, higher production yields, and applications in the hydrogen safety and flare emissions monitoring spaces.

03 NATURAL GAS↗

DOE OSTI2024

Integration of Decentralized Graph-Based Multi-Agent Reinforcement Learning with Digital Twin for Traffic Signal Optimization

Machine learning (ML) methods, particularly Reinforcement Learning (RL), have gained widespread attention for optimizing traffic signal control in intelligent transportation systems. However, existing ML approaches often exhibit limitations in scalability and adaptability, particularly within large traffic networks. This paper introduces an innovative solution by integrating decentralized graph-based multi-agent reinforcement learning (DGMARL) with a Digital Twin to enhance traffic signal optimization, targeting the reduction of traffic congestion and network-wide fuel consumption associated with vehicle stops and stop delays. In this approach, DGMARL agents are employed to learn traffic state patterns and make informed decisions regarding traffic signal control. The integration with a Digital Twin module further facilitates this process by simulating and replicating the real-time asymmetric traffic behaviors of a complex traffic network. The evaluation of this proposed methodology utilized PTV-Vissim, a traffic simulation software, which also serves as the simulation engine for the Digital Twin. The study focused on the Martin Luther King (MLK) Smart Corridor in Chattanooga, Tennessee, USA, by considering symmetric and asymmetric road layouts and traffic conditions. Comparative analysis against an actuated signal control baseline approach revealed significant improvements. Experiment results demonstrate a remarkable 55.38% reduction in Eco_PI, a developed performance measure capturing the cumulative impact of stops and penalized stop delays on fuel consumption, over a 24 h scenario. In a PM-peak-hour scenario, the average reduction in Eco_PI reached 38.94%, indicating the substantial improvement achieved in optimizing traffic flow and reducing fuel consumption during high-demand periods. These findings underscore the effectiveness of the integrated DGMARL and Digital Twin approach in optimizing traffic signals, contributing to a more sustainable and efficient traffic management system.

42 ENGINEERING↗

DOE OSTI2024

Integration of Decentralized Graph-Based Multi-Agent Reinforcement Learning with Digital Twin for Traffic Signal Optimization

actuated signal control↗

DOE OSTI2024

Few measurement shots challenge generalization in learning to classify entanglement

The ability to extract general laws from a few known examples depends on the complexity of the problem and on the amount of training data. In the quantum setting, the learner's generalization performance is further challenged by the destructive nature of quantum measurements that, together with the no-cloning theorem, limits the amount of information that can be extracted from each training sample. In this paper we focus on hybrid quantum learning techniques where classical machine-learning methods are paired with quantum algorithms and show that, in some settings, the uncertainty coming from a few measurement shots can be the dominant source of errors. We identify an instance of this possibly general issue by focusing on the classification of maximally entangled vs. separable states, showing that this toy problem becomes challenging for learners unaware of entanglement theory. Finally, we introduce an estimator based on classical shadows that performs better in the big data, few copy regime. Our results show that the naive application of classical machine-learning methods to the quantum setting is problematic, and that a better theoretical foundation of quantum learning is required.

97 MATHEMATICS AND COMPUTING↗